His first coaching job in NFL was as the defensive coordinator for the Chicago Bears in 1986, one year following their legendary 1985 Super Bowl winning season. Tobin filled the role left by legendary defensive coordinator Buddy Ryan, who had left the team to become the head coach of the Philadelphia Eagles. While the Bear's defensive unit ranked among the league's highest during his tenure, they never achieved the same dominance as they did in 1985, the teams one playoff win coming over Ryan's Eagles in 1988's Fog Bowl. Following the 1992 firing of head coach Mike Ditka, Tobin was released with the rest of the Bears coaching staff.

He was the head coach of the Cardinals in 1996 and succeeded Buddy Ryan again. His one winning season and playoff berth as a head coach came in 1998 where the club posted a 9-7 record. He then coached the Cardinals to their first playoff win in 50 years during the 1998 season by defeating the 3rd-seeded Dallas Cowboys. The team lost the next week to the 1st-seeded Minnesota Vikings. After 7 games into the 2000 season, Tobin was fired after posting a 2-5 record. His record in Arizona was 28-43, with a 1-1 post season record.